Table 2.

Uncorrected Fisher's LSD test comparing differences between persistent and non-persistent (on way) in positions showing a median of variability higher than 25%. Spike domain in bold character. CI: confidence interval; LSD: least significant difference; Diff.: differences.

Position in SARS-CoV-2 genome	Predicted mean diff	95.00% CI of diff	Below threshold?	Summary	Individual P Value
77	3.892	0.9903 to 6.793	Yes	**	0.0086
78	3.578	0.6766 to 6.479	Yes	*	0.0157
79	3.888	0.9865 to 6.789	Yes	**	0.0086
84	7.875	4.973 to 10.78	Yes	****	< 0.0001
227	3.568	0.6669 to 6.470	Yes	*	0.0159
307	4.855	1.954 to 7.757	Yes	**	0.0010
435	0.6604	− 2.212 to 3.533	No	ns	0.6522
803	0.7572	− 2.115 to 3.629	No	ns	0.6054
942	− 0.3859	− 3.258 to 2.486	No	ns	0.7923
1067	1.868	− 1.004 to 4.741	No	ns	0.2023
1091	1.513	− 1.359 to 4.385	No	ns	0.3018
1131	0.9277	− 1.945 to 3.800	No	ns	0.5267
1420	4.918	2.046 to 7.791	Yes	***	0.0008
1629	− 0.9281	− 3.800 to 1.944	No	ns	0.5265
1814	− 1.049	− 3.921 to 1.823	No	ns	0.4741
2130	0.07450	− 2.798 to 2.947	No	ns	0.9595
2494	− 0.4290	− 3.301 to 2.443	No	ns	0.7697
3037	4.013	1.141 to 6.886	Yes	**	0.0062
3413	− 3.637	− 6.509 to − 0.7649	Yes	*	0.0131
3833	− 3.312	− 6.184 to − 0.4392	Yes	*	0.0238
3902	0.7680	− 2.104 to 3.640	No	ns	0.6002
3903	0.4281	− 2.444 to 3.300	No	ns	0.7702
4175	1.207	− 1.665 to 4.079	No	ns	0.4102
4322	2.025	− 0.8476 to 4.897	No	ns	0.1671
4370	− 2.125	− 4.997 to 0.7477	No	ns	0.1471
4383	− 0.02589	− 2.898 to 2.846	No	ns	0.9859
5100	− 1.508	− 4.385 to 1.369	No	ns	0.3043
5225	− 1.835	− 4.712 to 1.042	No	ns	0.2113
5305	− 2.140	− 5.012 to 0.7327	No	ns	0.1443
6078	− 0.4271	− 3.299 to 2.445	No	ns	0.7707
6306	0.4119	− 2.460 to 3.284	No	ns	0.7786
6962	− 0.7172	− 3.604 to 2.169	No	ns	0.6262
7225	− 1.991	− 4.864 to 0.8809	No	ns	0.1742
7814	− 3.393	− 6.265 to − 0.5204	Yes	*	0.0206
7815	− 1.610	− 4.482 to 1.263	No	ns	0.2721
8377	0.07948	− 2.793 to 2.952	No	ns	0.9567
8607	− 2.670	− 5.542 to 0.2024	No	ns	0.0685
9027	− 1.021	− 3.893 to 1.852	No	ns	0.4861
9475	4.372	1.499 to 7.244	Yes	**	0.0029
9539	1.957	− 0.9150 to 4.830	No	ns	0.1817
9628	− 2.102	− 4.975 to 0.7700	No	ns	0.1514
9681	− 0.4431	− 3.315 to 2.429	No	ns	0.7624
9812	− 3.660	− 6.533 to − 0.7881	Yes	*	0.0125
10,528	− 0.6040	− 3.476 to 2.268	No	ns	0.6802
10,606	1.681	− 1.192 to 4.553	No	ns	0.2515
11,075	− 1.257	− 4.129 to 1.616	No	ns	0.3912
11,076	0.1884	− 2.684 to 3.061	No	ns	0.8977
11,096	1.235	− 1.637 to 4.107	No	ns	0.3993
11,743	0.8390	− 2.033 to 3.711	No	ns	0.5670
11,991	− 0.5595	− 3.432 to 2.313	No	ns	0.7026
12,197	− 1.699	− 4.571 to 1.174	No	ns	0.2464
12,437	0.5408	− 2.331 to 3.413	No	ns	0.7121
13,124	− 0.5118	− 3.384 to 2.360	No	ns	0.7269
13,163	1.664	− 1.208 to 4.536	No	ns	0.2562
13,164	1.644	− 1.229 to 4.516	No	ns	0.2620
13,476	0.5222	− 2.350 to 3.394	No	ns	0.7216
13,492	4.814	1.941 to 7.686	Yes	**	0.0010
13,584	2.656	− 0.2166 to 5.528	No	ns	0.0700
13,587	− 0.7122	− 3.584 to 2.160	No	ns	0.6270
13,709	0.8719	− 2.000 to 3.744	No	ns	0.5519
15,955	1.539	− 1.333 to 4.411	No	ns	0.2936
16,631	− 2.319	− 5.200 to 0.5629	No	ns	0.1148
17,045	2.137	− 0.7350 to 5.010	No	ns	0.1447
17,100	− 0.2866	− 3.159 to 2.586	No	ns	0.8449
18,315	2.474	− 0.3982 to 5.346	No	ns	0.0914
18,369	0.8906	− 1.982 to 3.763	No	ns	0.5434
19,484	9.076	6.070 to 12.08	Yes	****	< 0.0001
19,984	− 2.243	− 5.145 to 0.6590	No	ns	0.1298
20,487	− 0.3043	− 3.177 to 2.568	No	ns	0.8355
20,488	− 0.8657	− 3.738 to 2.007	No	ns	0.5547
20,679	5.523	2.651 to 8.396	Yes	***	0.0002
20,931	3.226	0.3535 to 6.098	Yes	*	0.0277
21,102	− 0.6568	− 3.529 to 2.215	No	ns	0.6540
21,409	− 5.408	− 8.294 to − 2.521	Yes	***	0.0002
21,422	3.274	0.3873 to 6.160	Yes	*	0.0262
21,635	1.193	− 1.684 to 4.070	No	ns	0.4162
21,876	− 0.5915	− 3.473 to 2.290	No	ns	0.6874
22,121	0.6094	− 2.272 to 3.491	No	ns	0.6785
22,131	8.987	6.106 to 11.87	Yes	****	< 0.0001
22,210	3.617	0.7354 to 6.499	Yes	*	0.0139
22,219	− 1.356	− 4.238 to 1.525	No	ns	0.3563
22,992	10.50	7.623 to 13.39	Yes	****	< 0.0001
23,104	− 0.5266	− 3.408 to 2.355	No	ns	0.7202
23,144	− 0.3490	− 3.231 to 2.533	No	ns	0.8124
23,231	− 2.356	− 5.238 to 0.5257	No	ns	0.1091
23,561	0.2884	− 2.593 to 3.170	No	ns	0.8445
23,836	− 1.838	− 4.720 to 1.044	No	ns	0.2113
23,904	− 0.6141	− 3.496 to 2.267	No	ns	0.6761
24,056	2.194	− 0.6872 to 5.076	No	ns	0.1355
24,057	2.740	− 0.1415 to 5.622	No	ns	0.0624
24,120	− 0.8981	− 3.780 to 1.984	No	ns	0.5413

Uncorrected Fisher's LSD	Predicted (LS) mean diff	95.00% CI of diff	Below threshold?	Summary	Individual P Value
24,199	3.730	0.8489 to 6.612	Yes	*	0.0112
24,245	− 1.297	− 4.179 to 1.584	No	ns	0.3775
24,290	2.245	− 0.6370 to 5.126	No	ns	0.1268
24,673	− 3.784	− 6.666 to − 0.9027	Yes	*	0.0101
24,718	− 1.418	− 4.299 to 1.464	No	ns	0.3349
25,101	− 2.456	− 5.337 to 0.4261	No	ns	0.0949
25,583	2.934	0.05215 to 5.815	Yes	*	0.0460
25,588	− 0.9908	− 3.872 to 1.891	No	ns	0.5003
25,798	0.09817	− 2.783 to 2.980	No	ns	0.9468
26,409	− 2.629	− 5.511 to 0.2525	No	ns	0.0737
26,431	0.9982	− 1.883 to 3.880	No	ns	0.4971
26,453	4.665	1.783 to 7.546	Yes	**	0.0015
26,455	3.789	0.9075 to 6.671	Yes	**	0.0100
26,461	5.185	2.303 to 8.066	Yes	***	0.0004
26,465	3.183	0.3018 to 6.065	Yes	*	0.0304
26,466	3.611	0.7298 to 6.493	Yes	*	0.0140
26,467	3.442	0.5600 to 6.323	Yes	*	0.0192
26,562	− 3.316	− 6.197 to − 0.4341	Yes	*	0.0241
26,746	0.08451	− 2.807 to 2.976	No	ns	0.9543
27,103	1.040	− 1.851 to 3.931	No	ns	0.4808
28,215	− 3.411	− 6.302 to − 0.5192	Yes	*	0.0208
28,331	2.988	0.09622 to 5.879	Yes	*	0.0428
28,637	− 0.1477	− 3.039 to 2.744	No	ns	0.9203
28,681	9.645	6.753 to 12.54	Yes	****	< 0.0001
28,699	0.009643	− 2.882 to 2.901	No	ns	0.9948
28,881	10.29	7.402 to 13.18	Yes	****	< 0.0001
29,196	2.127	− 0.7647 to 5.018	No	ns	0.1494
29,219	1.347	− 1.544 to 4.239	No	ns	0.3610
29,387	0.8119	− 2.089 to 3.713	No	ns	0.5833
29,701	− 0.5959	− 3.487 to 2.295	No	ns	0.6863
29,777	0.3283	− 2.563 to 3.220	No	ns	0.8239
29,801	2.255	− 0.6366 to 5.146	No	ns	0.1264

Significant values are in bold and italics.